howto is a script for simplifying running commands from Docker and Singularity images, Conda environments, or natively.

Prerequisites

howto is meant to be a wrapper for Docker, Singularity, and/or Conda, so ideally some combination of these should be installed on your system.

The howto script is written in Perl and relies on a handful of external libraries that should be part of the Perl core.

Installation

Just put the howto and find-closest-ancester-dir scripts somewhere on your $PATH.

Specifying the packages and their commands.

The howto script looks for a YAML file that lists the known Docker packages and the commands that each provide. The howto scripts looks for the YAML file in each of these locations, in this order:

• The file specified with the -f argument.
• ./howto.yaml
• ./.howto.yaml
• ~/.howto.yaml

An example YAML file, howto.sample.yaml, is provided.

Environment variables

The howto script used Singularity by default, but this can be override by setting the following environment variable,

export HOWTO_BACKEND=docker

Usage

The basic way to run a command that is provided by a container is,

howto cmd arg1 arg2 ...

The script is able to map commands to containers using 'howto.yaml' (also attached).

Here's how it might work,

# select the Docker backend; Singularity is the default
export HOWTO_BACKEND=docker

# pull all of the containers specified in howto.yaml. Both
# Singularity and Docker containers are cached, so you should only
# have to do this once.
howto -p '*'

# List all known commands (and their containers)
howto -l

# Run a command, in this case, `SearchGUI` from the
# `pvstodghill/searchgui:3.2.6__2017-02-01`
howto SearchGUI --help

# List all of the options
howto -h